Biology - the study of life

What is Life?

Life as a word is difficult to define because the living state is not a clear-cut condition.
Rather, it is a continuum upon which many objects exist. There are some fundamental properties
that, taken together abundantly, constitute the living condition. Certain objects possess all
of these properties and are obviously alive. We call these objects organisms. Other items
in our universe possess only some of these properties and are considered to a greater or
lesser extent non-living.

During this course we will examine each of these properties to some extent. For now we will
content ourselves with just the first...cellular structure. All truly living things
are composed of cells. These are microscopic chambers that each contain the "stuff" of life.
In fact, the smallest organisms consist of just one cell! These unicellular organisms are
found generally in the two Kingdoms called Monera and Protista. As organisms, these single
cells carry out all of the properties of life listed above! Thus the cell is a unit
of life.

It is important to realize, however, that in multicellular organisms such as higher plants
and humans there are cells that lack certain properties. In fact some cells function best
when they are totally dead as we shall soon see...

Cells = the unit of life

"Typical" Cell Structure

The cell shown below is called a parenchyma cell. It is perhaps typical of those found in
the soft cells of all plants. A herbaceous plant (such as a grass) might be 90% parenchyma.
A woody plant (such as a tree) might be less than 30% parenchyma.

As you can see in the diagram above, a plant cell has an outer boundary that includes a
cell wall. This cell wall is unique to the range of organisms called plants...animal
cells do not have cell walls! This wall is a boundary between the cell and its environment.
Just like any good wall, it keeps out any invaders and other cells. But again, just like
any good boundary, it is meant to be crossed. In fact the import and export of materials
is critical to the life of the cell. So a wall is only as good as its doors and windows.
This lesson was not well appreciated by Soviet states and ancient China. The exchange of
materials and ideas provides vitality to what is within the wall. Without this exchange
death is really the only option. The plant cell wall is quite passive really. It is
made up of cellulose (an indigestible--by humans--polysaccharide carbohydrate)
and other polymers of sugar. The fibrils of cellulose form a loose basket-weave
arrangement through which materials can filter in or out without further barrier.
It serves more of a filtration function than a control function. The other polymers
in the wall area may include pectin (a polygalacturonan) that serves as the
glue to hold one plant cell firmly to an adjacent cell. In fact the outer layer of
higher plant cells is sometimes called the middle lamella because this heavy
layer of pectin glue is quite visible in electron microscope images of plant tissues.
Humans extract pectin and use it to thicken fruit juices into a material called jam
or jelly (depending on the presence or absence of fruit pulp). You can buy Certo or
Sure-Jell in the grocery store to use in jelly-making; these are purified forms of
pectin--plant cell glue.

Just inside the cell wall is the cell membrane.
This membrane is made up of phospholipids (such as lecithin) and membrane-proteins.
This thin "skin" of the cell is the important import/export control area.
The phospholipids provide the barrier functions. Their hydrophilic polar "heads"
face the inside and outside of the membrane and prevent passage of hydrophobic
substances through the membrane. The phospholipid hydrophobic "tails" face the
middle of the membrane layer and prevent the passage of hydrophilic substances
through the membrane. Thus the layered form of the membrane is a pretty good
barrier to most chemicals. Special proteins made by the cell serve as windows
and doors in this membrane. These transport proteins have both hydrophobic
sections that align inside the membrane and hydrophilic sections that align with
the inner and/or outer membrane surfaces. By bridging both the hydrophilic and
hydrophobic regions of the membrane, these proteins are "bound" to the membrane.
Most interestingly, however, is that these bridging proteins can form channels
through the membrane for a particular kind of chemical to pass. In fact, some of
the membrane proteins can energetically grasp chemicals and actively pump them
across the membrane to the other side! These transport proteins are sometimes
called active transport carriers. Thus membrane proteins are those all-important
doors and windows through the barrier!

Moving to the middle of the cell somewhere we find a double membrane surrounding
a region of fluid which contains DNA. This structure is called the nucleus.
Please note the spelling and pronunciation (new-clee-us...NOT...new-kew-lus);
learning correct pronunciation will help correct spelling (probably, library,
and February are also commonly mispronounced and misspelled). Nothing makes you
sound more ignorant of your studies than mispronunciation of its critical
vocabulary. The nucleus processes information held in the DNA molecules that
it contains. Sometimes the nucleus copies the DNA into new molecules of DNA in
preparation for cell division; this process is called replication.
Replication is a critical prelude to making two cells from just one and so is
tied directly to reproduction and inheritance from one generation to the next.
A more mundane function of the nucleus is to make an RNA copy of the DNA;
this process is called transcription. The DNA is a more-or-less permanent
copy of critical information; it might be thought of as master plans for the cell.
When these master plans are to be used, they are transcribed into an inexpensive
and disposable copy in RNA...a kind of blueprint to be handled, used, and
ultimately destroyed. These RNA blueprints are sent out from the nucleus to be
acted upon by other parts of the cell.

Just outside the nucleus and extending out to the cell membrane is an area often
referred to as cytoplasm. We will avoid this all-encompassing term because
it gives the idea that this part of the cell is somehow a uniform fluid. Indeed
to ancient biologists using light microscopes this region did seem pretty
homogenous--hence one word to describe it. With the advent of the electron
microscope we have discovered other structures floating in this region of the
cell and so we generally avoid the term cytoplasm. In its place we
simply use cytosol to refer to the liquid around all of the floating
structures between the nucleus and cell membrane. The cytosol is mostly water,
but significantly contains many dissolved substances. Notable among these
substances are enzymes. Enzymes are proteins that cause certain chemical
reactions to occur at a much faster rate. These enzymes might build materials
(anabolism) or take apart materials (catabolism) in the cell, depending upon
the kind of enzyme in observation. Thus these enzymes are involved in the
chemical processing that actively takes place in the cytosol. The whole of
these processes is called metabolism; anabolism and catabolism are two opposing
categories of metabolism. Thus much "work" is done in the cytosolic fluid of cells!

Some of the floating membranes in the cytosol include a network of tiny tubes that
interconnect throughout the inside of the cell. This network is called
endoplasmic reticulum...literally a network inside the fluid of the cell.
This network is involved in the transport of materials from one part of the cell to
another, and maintains the integrity of the membranes surrounding the nucleus.
This is the conveyor belt of the cell.

On the surface of some of the endoplasmic reticulum are thousands of tiny
structures in the cytosol called ribosomes. These ribosomes are made of
protein and RNA and are actively involved in the synthesis of proteins. The
ribosome attaches to the RNA blueprints coming out from the nucleus. It reads
the information coded in the sequence of bases in the RNA and, using this
information, assembles a particular protein. Ribosomes are thus a kind of
protein-synthesis "machine." This process of using the information in RNA
to make a protein is called translation; it is the complement of
transcription. The protein products of the translation include the enzymes
("workers") of the cell. These proteins are shipped throughout the cell
for functional uses.

The endoplasmic reticulum near the ribosomes is responsible for moving much
of the protein through its tubules to other parts of the cell. One area of
particular importance on the fringes of the endoplasmic reticulum is the
Golgi apparatus or dictyosome. Here the proteins arrive and
are sorted by tagging with sugars or lipids, and are packaged into tiny
membrane-bound packages called vesicles. The Golgi apparatus thus
is a sorting and packaging structure. Depending upon contents, these
vesicles move to a particular destination and the membranes fuse. The
contents of the vesicle are thus "dumped" to the other side of the receiving membrane.

This vesicular transport process explains how proteins made by the cell might
be dumped through the cell membrane to the outside environment. Such a process
is called exocytosis; literally a process pushing materials outside of
the cell. On the other hand, vesicles can also be formed at the cell membrane
by engulfing materials on the outside of the cell to bring to the inside. Such
an import process would be called endocytosis if the material is particulate.
In the special case of vesicular import of only water and dissolved chemicals,
the process is named pinocytosis; literally cell drinking. Vesicular
transport adds to the repertoire and to the scale of the import/export
operations carried out at the cell membrane.

To drive almost all of the processes described above, we need energy. In animals
there is one energy powerhouse...the mitochondrion. This structure has a
smooth outer membrane and a convoluted inner membrane. The mitochondrion imports
fuel molecules (chiefly acetyl Co-enzyme A) to be converted into carbon dioxide
and water. This process requires the presence of oxygen and is called respiration:

CH2O + O2 --------> CO2 + H2O + energy

You might notice that this process is essentially the reverse of photosynthesis
(though drastically different in details!) and releases energy instead of requiring
the input of light energy. This release of energy from the respiration in the
mitochondrion allows for all the work done in the cell. All living cells with a
true nucleus (the eukaryotic cells), including those of plants, contain
mitochondria and carry out respiration. Yes, again, plants have mitochondria and
they do respiration both day and night! Many people are unaware of this fact...now you know!

It is easy to understand how the cell gets its oxygen from the atmosphere, but from where
does it get the carbohydrate (CH2O)? In the case of fungi and animals, the
fuels for respiration come from digestion of plant-derived foodstuffs found (or hunted -down!)
in the environment. For plants, the carbohydrate can come from that essentially reverse
process, photosynthesis:

CO2 + H2O + light -------> CH2O + O2

Photosynthesis occurs in the chloroplast of the cell. This structure floating in the
cytosol has two smooth outer membranes and a system of stacks of membranes inside.
The whole chloroplast is some ten times larger than a mitochondrion, and it stacks
of membranes inside are called grana. These grana are composed of many
individual membrane sacs called thylakoid membranes. Each thylakoid membrane
has special proteins that hold molecules of the green pigment chlorophyll.
This chlorophyll is responsible for trapping the energy of the light to use in driving
the production of carbohydrates in photosynthesis. We shall learn more of this process
later in the term. For now, let's just remember that plants have both
mitochondria and chloroplasts and therefore can do both respiration and
photosynthesis! Animals lack chloroplasts.

Finally in our brief tour of cell structure and function, let us remember that all
processes described here produce waste materials, and this leads us to one more
distinction between plants and animals. Typically animals use various processes
to dump their wastes to the environment. Single-celled animals may use vesicular
transport to rid themselves of waste by exocytosis. Higher animals concentrate
wastes through a urinary system and then urinate periodically in the environment.
Since a plant produces great food for an animal to eat, you might not be surprised
to find that plants hold their toxic wastes. This way a grazing animal gets a
dose of poison every time it tries to eat the plant. The toxic wastes of a
plant cell are stored in the vacuole. This central region is surrounded
by a membrane (the tonoplast) that selectively pumps cellular wastes and
poisons into the vacuole. Early botanists mistakenly thought the vacuole was
pretty empty and uninteresting...hence the name vacuole...but now we know that
this is a very interesting place where some pretty important metabolism occurs.
Certain materials are recycled back out of the vacuole after detoxification
reactions. Others are converted to even more-toxic forms once they reach the
inside of the vacuole. Yet others are crystallized into raphides or other
forms that pierce animal digestive systems or otherwise cause hemorrhage inside
the herbivore. The vacuole is certainly not a vacuum nor void of interest!

There are many details left out of this brief description of cell structure and
function, but at least we have made a start. One good way to think about the
parts and functions of cells is to think of the cell as a business. How would
you organize a factory that was making and exporting a particular product? A
cell is well-designed to do this...

Another important way to study is to think about the three fundamental structures
listed above that are unique to plants. Which ones are they?

Organelles unique to plants:

Cell Wall

Chloroplast

Vacuole

Note: the above are in addition to the usual organelles found in animal cells.
Plants are MORE...not less....than animal cells!

Finally, a good way to study cell structure and function is by means of a concept map.
Here is a crude concept map showing the relationships between the parts in terms of
functions.

Cell Functions - A concept map:

I mentioned above that the smallest plants consisted of single cells. The largest organism
on our planet is the sequoia tree. This tree is larger than 10 blue whales (the largest
animal) and so is easily the largest obvious organism. Certain fungi in soil, however,
consist of microscopic but connect filaments of cells originating from a single spore.
These fungi are basically invisible, but DNA evidence suggests that single individuals
may spread across hundred of acres of land. So these fungi may, in fact, be the
"largest" organisms.

In terms of lifespan, some cells (and unicellular organisms) live for only a few minutes
before dividing and making new cells or perishing altogether. Some multicellular
organisms can live to be very old. The oldest documentable living organism is the
bristlecone pine tree. These trees are frequently more than 5000 years old. They were
already older than any extant human when the pyramids were built in Egypt! These plants,
still alive today, were already 3000 years old when Jesus walked through Jerusalem.
Admittedly, some clonal plants are harder to document and may be even older than the
bristlecone pine, but the age of the bristlecone pine is easy to document!

Other Cell Types:

You might be misled into thinking that the "typical" cell is most of what is available
or most of what is important. This couldn't be farther from the truth! Plant cells
can be classified into four fundamental cell types (and many other specific kinds).

Meristematic Cells undergo mitosis and thereby produce all cells of the plant body.
Mitosis is the nuclear division (usually followed by cytokinesis) that results in
the production of new cells. Mitosis is a process in which a cell goes from
interphase, through prophase, metaphase, anaphase, and telophase, and ends up
in interphase again. The cell division process assures that the master plans in
the DNA of the nucleus are replicated accurately and completely, and that the
copies of the master plans are evenly divided between the two resulting cells
in an orderly fashion. This ensures the integrity and completeness of the master
plans in both of the cells.

Derivatives of meristematic cells can mature in any one of three directions...only
one of which results in a "typical" cell (parenchyma):

It might not be completely obvious, but study of the diagram above will reveal
that some cells are long and thin, some cells have thin walls and others have
thick walls, and some cells are alive and others are dead!

Indeed dead cells can be useful to a multicellular organism. In humans, dead
cells contribute the structure of hair shafts and nails. In plants dead cells
provide stony protective layers in peach pits and the conductive elements of
the xylem. Without the dead xylem elements, a plant would literally cook in
the sun because it would lack the water from the xylem to efficiently cool
the leaves by evaporation of that water. Without the dead xylem to bring
minerals up with that water, plants would lack essential metal ions from
the soil. These soil minerals include calcium, magnesium, iron, and zinc
(more on those later in the course!). Our food would lack some of its
essential nutrition were it not for these dead cells in plants!